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<h2>SyMAP Queries</h2>
<p>
This page allows you to query many aspects of the alignment and synteny 
between species, in order to transfer information between species,
improve annotations, and understand the expansion and contraction
of gene families. 
<p> 
The query occurs in three stages, corresponding to the section numbers
on the Query Page. Each stage has its own filters. 

<h3>1. Filter hits</h3>

The first stage is to retrieve hits (anchors) from the database, based on 
filters such as chromosome and annotation string. Note that each anchor
connects two species and hence represents a <i>pair</i> of putatively-related
regions on the two species. Filters are as follows:

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<b>Annotation String Search</b>
<p>
Enter annotation search terms. Hits will be returned which overlap a matching annotation
on either side. 
<p>
<b>Chromsome/location filters</b>
<p>
Each selected species has a row in which you can select to search either all
its sequences, or a particular sequence or basepair region.
<p>
<b>Only synteny hits</b>
<p>
Return only hits which are part of a syntenic block. This
helps to screen false positive hits, but can also conceal true hits that are not
part of a detectable syntenic block. (Note that SyMAP hits are already filtered
during loading using a reciprocal-top-2 filter.)
<p>
<b>Only hits in a collinear gene pair</b>
<p>
Return only hits which are part of a pair of aligning genes having no intervening
non-aligning genes. This relates to the RunSize column, which is one of the optional
columns of the Query Result table. RunSize shows the size of collinear chain which 
a hit is contained in, hence this checkbox is equivalent to RunSize at least 2. 
Note that a collinear chain is not the same as a SyMAP synteny block, because blocks
require at least 7 anchors, and are allowed to have intervening genes which do not align.
<p>
<b>Show orphan genes</b>
<p>
If checked, then the results will show all genes which <i>do not</i> overlap any of the hits
matching the search criteria (i.e, the hits which would be shown in the table if this
checkbox were not checked). Note that the genes must also meet the search criteria,
e.g. matching the annotation query string and the chromosome location requirements. 

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<p>

<h3>2. Filter putative gene families (PgeneFs)</h3>

Using the hits that pass the Stage 1 filters, SyMAP constructs putative gene families (PgeneFs) 
spanning the selected species. This is done by grouping hits which overlap on at 
least one genome. <i>Note, if you have more than 6 species selected, this stage can take
an hour or more.</i>
<p>
Each PgeneF is given a number, which is shown in the Query Results table (column name "PgeneF"). 
The size of the PgeneF is also shown (column "PgFSize"). 
<p>
Filters at this stage apply to the PgeneF as a whole:

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<b>Include/Exclude</b>
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These filters permit searching for gene families shared by one group of species but not
present in another. 
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If a species is checked to include, then the PgeneF will only be retained if it includes
at least one hit which hits that species. 
<p>
If a species is checked to exclude, then the PgeneF will be discarded if any of its
hits are to that species. 
<p>
<b>No annotation to included species</b>
<p>
Find PgeneFs which are not yet annotated. A PgeneF will be discarded if it is annotated on any of
the species which are checked in the <b>Include</b> line.
<p>
<b>Complete linkage of included species</b>
<p>
Require the PgeneF to be fully linked, i.e. for each pair of species A and B in the group,
there must be a hit linking A to B.  
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<p>

<h3>3. Filter displayed hits</h3>

The query returns hits between all pairs of the selected species; however, you may
only be interested in seeing those which hit certain species. To achieve this,
select those species in the <b>Include</b> row of Filter Stage 2, and also check
the box below, <b>Show only hits to the included species</b>. Only those hits will be shown,
although the PgeneF numbers will reflect groupings created using all hits. 

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